Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_011188973.1 DP_RS08825 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000025945.1:WP_011188973.1 Length = 435 Score = 388 bits (996), Expect = e-112 Identities = 190/426 (44%), Positives = 277/426 (65%), Gaps = 1/426 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 MK + +G++G GTVG G A LR E + R+G IR+ + D++ + + Sbjct: 1 MKEICVGIIGFGTVGRGLAETLRIQQERLEARIGATIRLKTVADIACKSLPEEFAGVTLT 60 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 ++ ++ ++D+VVEL GG AK +L+AIENGKH++TANK LL+ +G EIF A Sbjct: 61 QNATDIFTDPEIDIVVELIGGIEPAKTFLLQAIENGKHVITANKALLSTHGKEIFEAAVA 120 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 +NV V FEA+V GGIP+IKAL+EGL ANRI SI GI+NGT+N+ILS+M E G+ FA+VLK Sbjct: 121 KNVEVGFEASVGGGIPVIKALKEGLVANRINSIKGIMNGTANYILSQMTEHGTPFAEVLK 180 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 EAQ LG+AEADPT+D+EG D HK+ I+ +A+G +N +EGIS ++ DI A E Sbjct: 181 EAQELGFAEADPTYDVEGVDTAHKLAILMTIAYGLNVNIDHINIEGISSIEPVDIDIARE 240 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 G+ IKLL ++ G +E RVHPT++P S +LA + G N + N D V + L YG GA Sbjct: 241 FGFAIKLLAISNNHGDNVEARVHPTMVPHSHMLATIGGAFNGIHFNGDTVTDVLLYGPGA 300 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 G +PT SAV AD+ DIAR + +D+ +RVP L++QP ++ A I PM E+ +YY R Sbjct: 301 GMMPTGSAVAADVADIARNILSDSVNRVPALSYQPERMTAPVITPMSELVCAYYFRFTVS 360 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD- 419 EPG L IA +L + N+S+++++QK + + +V+ +H E + +A+A I LD Sbjct: 361 SEPGVLAAIATILGKYNISVQSIVQKELGEDQPVYLVVRSHDAQESAVNAAMAEIRVLDA 420 Query: 420 CVEKPI 425 C+ +P+ Sbjct: 421 CLAEPL 426 Lambda K H 0.318 0.135 0.369 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 458 Number of extensions: 19 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 435 Length of database: 435 Length adjustment: 32 Effective length of query: 403 Effective length of database: 403 Effective search space: 162409 Effective search space used: 162409 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory